Ten-man Australia scored from the penalty spot with 20 minutes left to rescue a point in their qualifier against the in-form Japanese on Tuesday.
The top two are guaranteed a Brazil 2014 berth and Neill believes they will outlast Iraq, Oman and Jordan.
"I'd be very surprised if these two teams don't go on to finish first and second in the group," Neill said. "But (there's) a lot of games to play and a lot of work to do."
In an enthralling contest between the two top-ranked Asian sides, Japan appeared to have grabbed the winner through Yuzo Kurihara in the 65th minute.
But the Australians, who had substitute Mark Milligan sent off after a second yellow card 10 minutes earlier, grabbed the equaliser when Luke Wilkshire blasted home from the spot on 70 minutes.
Australia coach Holger Osieck was happy with a point, and Everton star Tim Cahill, who teamed superbly with Alex Brosque up front, felt the same.
"We started off really well, we dominated the play," said Cahill, who has been linked with a move away from the English Premier League to clubs in the Middle East and China.
"But circumstances with the sending off and things like that, we fought really hard and in the end it was a good result."